Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.010G053000.4-JGI_221_v2.1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3233
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Found at i:565 original size:3 final size:3
Alignment explanation
Indices: 559--686 Score: 157
Period size: 3 Copynumber: 42.7 Consensus size: 3
549 TCAGCAACAA
* * * * *
559 CAG CAG CAG CAA CAA CAG CAG CAG CAA CAA CAG CAG CAG CAG CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
607 CAG CAG CAG CAG CAG CAA CAA CAG CAG CAG CAG CAA CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
655 CAG CAG CAA CAA CAG CAA CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
687 ACAACAACAA
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.42, C:0.34, G:0.24, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:570 original size:15 final size:15
Alignment explanation
Indices: 550--724 Score: 191
Period size: 15 Copynumber: 12.1 Consensus size: 15
540 GAGGCATGCT
550 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
565 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
580 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
*
595 CAGCAGCAACAGCAG
1 CAGCAACAACAGCAG
610 CAG------CAGCAG
1 CAGCAACAACAGCAG
619 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
*
634 CAGCAGCAACAGCAG
1 CAGCAACAACAGCAG
* * *
649 CAGCAGCAGCAGCAA
1 CAGCAACAACAGCAG
* *
664 CAACAGCAACAGCAG
1 CAGCAACAACAGCAG
* * *
679 CAGCAGCAACAACAA
1 CAGCAACAACAGCAG
* * *
694 CAACAACAACAACAA
1 CAGCAACAACAGCAG
709 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
724 C
1 C
725 CGCAGCAGCA
Statistics
Matches: 139, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
9 9 0.06
15 130 0.94
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (15 bp):
CAGCAACAACAGCAG
Found at i:580 original size:18 final size:18
Alignment explanation
Indices: 553--731 Score: 187
Period size: 18 Copynumber: 9.9 Consensus size: 18
543 GCATGCTCAG
*
553 CAACAACAGCAGCAGCAA
1 CAACAGCAGCAGCAGCAA
*
571 CAACAGCAGCAGCAACAA
1 CAACAGCAGCAGCAGCAA
* * *
589 CAGCAGCAGCAGCAACAG
1 CAACAGCAGCAGCAGCAA
*
607 CAGCAGCAGCAGCAGCAA
1 CAACAGCAGCAGCAGCAA
625 CAACAGCAGCAGCAGCAA
1 CAACAGCAGCAGCAGCAA
* *
643 CAGCAGCAGCAGCAGCAG
1 CAACAGCAGCAGCAGCAA
* * *
661 CAACAACAGCAACAGCAG
1 CAACAGCAGCAGCAGCAA
* * * *
679 CAGCAGCAACAACAACAA
1 CAACAGCAGCAGCAGCAA
* * *
697 CAACAACAACAACAGCAA
1 CAACAGCAGCAGCAGCAA
*
715 CAACAGCAGCCGCAGCA
1 CAACAGCAGCAGCAGCA
732 GCAGTCGCCC
Statistics
Matches: 137, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 137 1.00
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (18 bp):
CAACAGCAGCAGCAGCAA
Found at i:691 original size:3 final size:3
Alignment explanation
Indices: 661--719 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
651 GCAGCAGCAG
* * * * *
661 CAA CAA CAG CAA CAG CAG CAG CAG CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
*
709 CAG CAA CAA CA
1 CAA CAA CAA CA
720 GCAGCCGCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.56, C:0.34, G:0.10, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:1553 original size:6 final size:6
Alignment explanation
Indices: 1542--1571 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1532 TGGCTCAGTT
1542 GCAACA GCAACA GCAACA GCAACA G-AACA G
1 GCAACA GCAACA GCAACA GCAACA GCAACA G
1572 TAGCTCACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.50, C:0.30, G:0.20, T:0.00
Consensus pattern (6 bp):
GCAACA
Done.